I can tell that you've been working hard at understanding the argument core on logical reasoning in general.
You have a perfectly reasoned counter to answer choice (E) if it stated
Apple Juice that undergoes intensive pasteurization contains less bacteria than McElligott's apple juice.
The conclusion is about the likelihood of containing bacteria - not the amount of bacteria contained.
We do know that intensive pasteurization eliminates bacteria more effectively than does any other method. (key word = eliminates)
Thus, since McElligott's apple juice is not intensive pasteurized it is not using the most effective method for eliminating bacteria and is therefore more likely to have bacteria present than apple juice that uses the most effective method - answer choice (E).
(A) is out of scope. The statements indicate nothing of the amount of bacteria contained in either the apple or citrus juices at McElligott's.
(B) is not known. We do know that McElligott's does not use the most effective method of eliminating bacteria, but we cannot compare the levels of bacteria between it's apple and citrus juices.
(C) is an issue of degree. We know about intensive pasteurization and it's affect on flavor, we have not been given information on other forms of pasteurization and their effects on flavor.
(D) is an issue of degree. We know that intensive pasteurization destroys flavor, but we do not know that it's the method most likely to destroy flavor. There could be some other method of pasteurization not discussed that destroys flavor more than intensive pasteurization.
(E) is correct for the reasons above.
#officialexplanation